DOCSLIB.ORG

The Role of the Seagrass Leaf Microbiome in Assisting Nitrogen Uptake by the Western Australian Seagrass, Posidonia Sinuosa

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Role of the Seagrass Leaf Microbiome in Assisting Nitrogen Uptake by the Western Australian Seagrass, Posidonia Sinuosa Edith Cowan University Research Online Theses: Doctorates and Masters Theses 2017 The role of the seagrass leaf microbiome in assisting nitrogen uptake by the Western Australian seagrass, Posidonia sinuosa Flavia Tarquinio Edith Cowan University Follow this and additional works at: https://ro.ecu.edu.au/theses Part of the Ecology and Evolutionary Biology Commons Recommended Citation Tarquinio, F. (2017). The role of the seagrass leaf microbiome in assisting nitrogen uptake by the Western Australian seagrass, Posidonia sinuosa. https://ro.ecu.edu.au/theses/2046 This Thesis is posted at Research Online. https://ro.ecu.edu.au/theses/2046 Edith Cowan University Copyright Warning You may print or download ONE copy of this document for the purpose of your own research or study. The University does not authorize you to copy, communicate or otherwise make available electronically to any other person any copyright material contained on this site. You are reminded of the following: Copyright owners are entitled to take legal action against persons who infringe their copyright. A reproduction of material that is protected by copyright may be a copyright infringement. Where the reproduction of such material is done without attribution of authorship, with false attribution of authorship or the authorship is treated in a derogatory manner, this may be a breach of the author’s moral rights contained in Part IX of the Copyright Act 1968 (Cth). Courts have the power to impose a wide range of civil and criminal sanctions for infringement of copyright, infringement of moral rights and other offences under the Copyright Act 1968 (Cth). Higher penalties may apply, and higher damages may be awarded, for offences and infringements involving the conversion of material into digital or electronic form. The role of the seagrass leaf microbiome in assisting nitrogen uptake by the Western Australian seagrass, Posidonia sinuosa Flavia Tarquinio M.Sc. in Marine Biology Polytechnic University of Marche This thesis is presented for the degree of Doctor of Philosophy School of Science Edith Cowan University 2017 USE OF THESIS The Use of Thesis statement is not included in this version of the thesis. ABSTRACT Microorganisms play a key role in facilitating the cycling of several elements in coastal environments, including nitrogen (N). N is a key component for maintaining high seagrass productivity and is often the limiting nutrient in marine environments. Seagrasses harbour an abundant and diverse microbial community (the ‘microbiome’), however their ecological and functional roles related to the seagrass host are still poorly understood, in particular regarding N cycling. Microorganisms capable of mineralising dissolved organic nitrogen (DON) may play a pivotal role in enhancing N availability in coastal environments such as seagrass meadows. Thus, the overall aim of my thesis was to enhance current understanding of abundance and diversity of the microbial community associated with seagrass meadows and their ecological role, with specific focus on N cycling. This was achieved by using molecular techniques together with 15N-enrichment experiments and nanoscale imaging techniques. Firstly, I reviewed the literature on the potential effects that microorganisms associated with both the above- and belowground seagrass tissue may have on plant fitness and the relevance of the seagrass microbiome and I have highlighted literature gaps. For my second chapter, I determined the abundance and community composition of bacteria and archaea associated with seagrass Posidonia sinuosa meadows in Marmion Marine Park, southwestern Australia. Data were collected from different seagrass meadows and meadow ‘microenvironments’, i.e. seagrass leaf surface, sediment and water column. I performed the quantitative polymerase chain reaction (q-PCR) targeting a series of bacterial and archaeal genes: 16S rRNA, ammonia oxidation genes (amoA) and genes involved in mineralisation of DON, via the urease enzyme (ureC). High-throughput sequencing was applied to 16S rRNA and amoA genes, to explore the diversity of these microbial assemblages related to P. sinuosa meadow microenvironments. Results from this chapter show that the P. II sinuosa leaf biofilm represents a favourable habitat for microorganisms, as it hosts a significantly higher microbial abundance compared to the sediment and water. Moreover, 16S rRNA and amoA sequencing data indicate a high degree of compartmentalisation of functional microbial communities between the microenvironments of the seagrass meadow (leaf, sediment and water column), pointing towards the existence of a core seagrass leaf microbiome that could have specific interactions with the plant. For my third chapter I determined the role that microorganisms inhabiting P. sinuosa seagrass leaves may play in the recycling of DON, and subsequent transfer of inorganic N (DIN) into plant tissues. To achieve this, I performed an experiment whereby seagrass leaves with and without microorganisms were incubated with DO15N, and I traced the fine-scale uptake and assimilation of microbially processed N into seagrass cells, using nanoscale secondary ion mass spectrometry (NanoSIMS). Results from this chapter show for the first time that seagrass leaf epiphytic microorganisms facilitated the uptake of 15N from DON, which was unavailable to the plant in the absence of epiphytes. This indicates that seagrass leaves have limited to no ability to take up DON, and the seagrass leaf microbiome could therefore play a much more significant role than previously thought in enhancing plant health and productivity. Finally, I determined the net nitrification rates associated with ammonia- oxidising microorganisms (AOM) inhabiting P. sinuosa leaf surfaces, and explored whether AOM facilitated, or competed for, the plant’s N uptake. My findings show + that AOM may compete with seagrasses for NH4 uptake, but that their potential to outcompete seagrass epiphytic algae for DIN uptake indicates that AOM on seagrass leaves may serve as a ‘biocontrol’ over excess epiphytic algal growth. In summary, the present thesis represents a significant advance in our understanding of the seagrass leaf-microbiome relationship and transformations of N within seagrass meadows. Moreover, it opens up new questions for future research not only on seagrass-microbiome interactions but other macrophytes in aquatic systems that may benefit from the presence of specific N-cycling microorganisms. III IV DECLARATION I certify that this thesis does not, to the best of my knowledge and belief: incorporate without acknowledgment, any material previously submitted for a degree or diploma in any institution of higher education; contain any material previously published or written by another person except where due reference is made in the text of this thesis; contain any defamatory material; or contain data that have not been collected in a manner consistent with ethics approval. Flavia Tarquinio August 2017 V This Thesis is Dedicated to My Family VI ACKNOWLEDGMENTS There are many people that helped me through this journey and that without them I would not have completed this thesis. First, I would like to thank my family for all the support. So probably noone will get offended if I write a couple of sentences in Italian! Grazie mille per tutto quello che avete fatto e farete per me, per sostenermi anche se siete lontani e per l’amore che continuo a ricevere, mi sembrate cosi vicini!!!Grazie a mia mamma mio padre e mio fratello vi voglio bene! Anche alle nonne, cosi non si offende nessuno! Now, a special thank to all my supervisors who have been working like crazy during the past weeks to allow me to get this work of art out in time! SO really thanks to all of you: Glenn Hyndes, Annette Koenders, Bonnie Laverock and Christin Sawstrom. You guys have been fantastic : ) A special thanks to all the researchers who also supported me during these years. Firstly, Megan Huggett, you did not just open your knowledge to me but also your home, so thanks : ) Thanks to Olly Berry who hosted me for a year at CSIRO in his fantastic lab and Jeremy Bougoure who gave me a free week run at the NasoSIMS (but don t tell anyone!) and was instrumental in helping me with Chapter 4. Thanks to Andrea Paparini who helped me through the sequencing at Murdoch University, but also for being there for my desperate calls. Also, thanks to Paul Guagliardo from the CMCA at UWA. A HUGE THANKS to La babba and Annina, friends before being colleagues, and thanks Duccio for feeding me in the last nights before thesis submission. Thanks to all of you my friends, in Italy (Lucy, Ros, Ca’ and Vale) and here (Ana, Chris, Bruno, Fede , Aldo, Giulia, all the CMER group) especially my good friend Titi, and sorry if I am not that precise/good, but I am going to send this thesis out in 15 so see you soon…….for a big party of course : D VII LIST OF PUBLICATIONS INCLUDED AS PART OF THE THESIS This thesis is presented as a series of manuscripts that are to be submitted for publication in international journals. I am the first author with a contribution of more than 50% to each publication. The thesis conforms to the “thesis with publication” style of Edith Cowan University. VIII IX Contents Use of thesis .................................................................................................................. i Declaration ................................................................................................................... v Acknowledgments.....................................................................................................
Load more

Recommended publications
  • Marine Microbiome As Source of Natural Products
    bs_bs_banner doi:10.1111/1751-7915.12882 Editorial: The microbiome as a source of new enterprises and job creation Marine microbiome as source of natural products Fernando de la Calle Department of Microbiology R&D, Pharma Mar S.A., Avda. de los Reyes, 1. Colmenar Viejo, 28770 Madrid, Spain. Less than 1% of living microorganisms can be cultured bioenergy and algal cosmetics and underestimate the in the laboratory, but even this minute part has produced role of the marine microbiome. Market opportunities and incredible discoveries such as antibiotics that have job creation are likely to significantly increase in the saved millions of lifes. We can only imagine what other future with the advent of transversal technologies direc- great inventions will come to light when the rest of this ted at exploiting other biotechnological advances, such enormous universe of living genomes is awakened. as the evolution of bioinformatics, synthetic biology, Everything is recorded in the genes, and modern molecular diagnostics and devices, biocatalysis and the metagenomic studies, involving the large-scale sequenc- many OMICS technologies. The marine microbiome ing of the genetic material of marine microorganisms, as must be an essential part of the bioeconomy. However, well as the similarities between the human gut and whilst the enormous potential of the marine microbiome ocean microbiomes, are not only providing powerful has been recognized by industry, there is currently a insights into why the Earth is a living planet, but are also lack of coordination amongst policy makers, govern- revealing possible causes and promising cures for meta- ments, civil society organizations, academia and large bolic diseases, including cancer.
    [Show full text]
  • Diatoms Shape the Biogeography of Heterotrophic Prokaryotes in Early Spring in the Southern Ocean
    Diatoms shape the biogeography of heterotrophic prokaryotes in early spring in the Southern Ocean Yan Liu, Pavla Debeljak, Mathieu Rembauville, Stéphane Blain, Ingrid Obernosterer To cite this version: Yan Liu, Pavla Debeljak, Mathieu Rembauville, Stéphane Blain, Ingrid Obernosterer. Diatoms shape the biogeography of heterotrophic prokaryotes in early spring in the Southern Ocean. Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2019, 21 (4), pp.1452-1465. 10.1111/1462-2920.14579. hal-02383818 HAL Id: hal-02383818 https://hal.archives-ouvertes.fr/hal-02383818 Submitted on 28 Nov 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Diatoms shape the biogeography of heterotrophic prokaryotes in early spring in the Southern Ocean 5 Yan Liu1, Pavla Debeljak1,2, Mathieu Rembauville1, Stéphane Blain1, Ingrid Obernosterer1* 1 Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650 10 Banyuls-sur-Mer, France 2 Department of Limnology and Bio-Oceanography, University of Vienna, A-1090 Vienna, Austria
    [Show full text]
  • Major Ocean Currents May Shape the Microbiome of the Topshell Phorcus
    www.nature.com/scientificreports OPEN Major ocean currents may shape the microbiome of the topshell Phorcus sauciatus in the NE Atlantic Ocean Ricardo Sousa1,2,3, Joana Vasconcelos3,4,5, Iván Vera‑Escalona5, João Delgado2,6, Mafalda Freitas1,2,3, José A. González7 & Rodrigo Riera5,8* Studies on microbial communities are pivotal to understand the role and the evolutionary paths of the host and their associated microorganisms in the ecosystems. Meta‑genomics techniques have proven to be one of the most efective tools in the identifcation of endosymbiotic communities of host species. The microbiome of the highly exploited topshell Phorcus sauciatus was characterized in the Northeastern Atlantic (Portugal, Madeira, Selvagens, Canaries and Azores). Alpha diversity analysis based on observed OTUs showed signifcant diferences among regions. The Principal Coordinates Analysis of beta‑diversity based on presence/absence showed three well diferentiated groups, one from Azores, a second from Madeira and the third one for mainland Portugal, Selvagens and the Canaries. The microbiome results may be mainly explained by large‑scale oceanographic processes of the study region, i.e., the North Atlantic Subtropical Gyre, and specifcally by the Canary Current. Our results suggest the feasibility of microbiome as a model study to unravel biogeographic and evolutionary processes in marine species with high dispersive potential. During the last decades we have observed an increase in the number of studies trying to elucidate the role of spe- cies and the environment where they live due to research expeditions and the use of several modern techniques to identify species, including genetic-based techniques 1. Early studies based on genetics focused on the description of species and populations but soon afer the frst results, it was evident that genetic-based studies could also be used to identify and describe major biogeographic patterns as well as to create the pathway to evaluate new hypotheses and ecological questions 2–4.
    [Show full text]
  • Corals and Sponges Under the Light of the Holobiont Concept: How Microbiomes Underpin Our Understanding of Marine Ecosystems
    fmars-08-698853 August 11, 2021 Time: 11:16 # 1 REVIEW published: 16 August 2021 doi: 10.3389/fmars.2021.698853 Corals and Sponges Under the Light of the Holobiont Concept: How Microbiomes Underpin Our Understanding of Marine Ecosystems Chloé Stévenne*†, Maud Micha*†, Jean-Christophe Plumier and Stéphane Roberty InBioS – Animal Physiology and Ecophysiology, Department of Biology, Ecology & Evolution, University of Liège, Liège, Belgium In the past 20 years, a new concept has slowly emerged and expanded to various domains of marine biology research: the holobiont. A holobiont describes the consortium formed by a eukaryotic host and its associated microorganisms including Edited by: bacteria, archaea, protists, microalgae, fungi, and viruses. From coral reefs to the Viola Liebich, deep-sea, symbiotic relationships and host–microbiome interactions are omnipresent Bremen Society for Natural Sciences, and central to the health of marine ecosystems. Studying marine organisms under Germany the light of the holobiont is a new paradigm that impacts many aspects of marine Reviewed by: Carlotta Nonnis Marzano, sciences. This approach is an innovative way of understanding the complex functioning University of Bari Aldo Moro, Italy of marine organisms, their evolution, their ecological roles within their ecosystems, and Maria Pia Miglietta, Texas A&M University at Galveston, their adaptation to face environmental changes. This review offers a broad insight into United States key concepts of holobiont studies and into the current knowledge of marine model *Correspondence: holobionts. Firstly, the history of the holobiont concept and the expansion of its use Chloé Stévenne from evolutionary sciences to other fields of marine biology will be discussed.
    [Show full text]
  • Tree-Aggregated Predictive Modeling of Microbiome Data
    www.nature.com/scientificreports OPEN Tree‑aggregated predictive modeling of microbiome data Jacob Bien1, Xiaohan Yan2, Léo Simpson3,4 & Christian L. Müller4,5,6* Modern high‑throughput sequencing technologies provide low‑cost microbiome survey data across all habitats of life at unprecedented scale. At the most granular level, the primary data consist of sparse counts of amplicon sequence variants or operational taxonomic units that are associated with taxonomic and phylogenetic group information. In this contribution, we leverage the hierarchical structure of amplicon data and propose a data‑driven and scalable tree‑guided aggregation framework to associate microbial subcompositions with response variables of interest. The excess number of zero or low count measurements at the read level forces traditional microbiome data analysis workfows to remove rare sequencing variants or group them by a fxed taxonomic rank, such as genus or phylum, or by phylogenetic similarity. By contrast, our framework, which we call trac (tree‑aggregation of compositional data), learns data‑adaptive taxon aggregation levels for predictive modeling, greatly reducing the need for user‑defned aggregation in preprocessing while simultaneously integrating seamlessly into the compositional data analysis framework. We illustrate the versatility of our framework in the context of large‑scale regression problems in human gut, soil, and marine microbial ecosystems. We posit that the inferred aggregation levels provide highly interpretable taxon groupings that can help microbiome researchers gain insights into the structure and functioning of the underlying ecosystem of interest. Microbial communities populate all major environments on earth and signifcantly contribute to the total plan- etary biomass. Current estimates suggest that a typical human-associated microbiome consists of ∼ 1013 bacteria1 and that marine bacteria and protists contribute to as much as 70% of the total marine biomass2.
    [Show full text]
  • A Community Perspective on the Concept of Marine Holobionts: Current Status, Challenges, and Future Directions
    A community perspective on the concept of marine holobionts: current status, challenges, and future directions Simon M. Dittami1, Enrique Arboleda2, Jean-Christophe Auguet3, Arite Bigalke4, Enora Briand5, Paco Cárdenas6, Ulisse Cardini7, Johan Decelle8, Aschwin H. Engelen9, Damien Eveillard10, Claire M.M. Gachon11, Sarah M. Griffiths12, Tilmann Harder13, Ehsan Kayal2, Elena Kazamia14, Francois¸ H. Lallier15, Mónica Medina16, Ezequiel M. Marzinelli17,18,19, Teresa Maria Morganti20, Laura Núñez Pons21, Soizic Prado22, José Pintado23, Mahasweta Saha24,25, Marc-André Selosse26,27, Derek Skillings28, Willem Stock29, Shinichi Sunagawa30, Eve Toulza31, Alexey Vorobev32, Catherine Leblanc1 and Fabrice Not15 1 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France 2 FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France 3 MARBEC, Université de Montpellier, CNRS, IFREMER, IRD, Montpellier, France 4 Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany 5 Laboratoire Phycotoxines, Ifremer, Nantes, France 6 Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden 7 Integrative Marine Ecology Dept, Stazione Zoologica Anton Dohrn, Napoli, Italy 8 Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRA, Grenoble, France 9 CCMAR, Universidade do Algarve, Faro, Portugal 10 Laboratoire des Sciences Numériques de Nantes (LS2N), Université
    [Show full text]
  • The Marine Microbiome Initiative
    The Marine Microbiome Initiative Justin Seymour, Martin Ostrowski, Mark Brown, Lev Bodrossy, Jodie van de Kamp, Andrew Bissett, Ana Lara-Lopez Seymour 2014 Emerging EOV: Microbial diversity and biomass Slides from Pier Buttigieg (via Ana Lara-Lopez) Evolution of the Marine Microbiome Initiative 2012 Australian Marine Microbe Biodiversity Initiative (AMMBI) NSI PHB MAI Evolution of the Marine Microbiome Initiative 2012 2014 Australian Marine Microbe BPA Marine Microbes Project Biodiversity Initiative (AMMBI) $1M DAR YON NSI NSI ROT PHB PHB KAI MAI MAI Evolution of the Marine Microbiome Initiative 2012 2014 2018 Australian Marine Microbe BPA Marine Microbes Project Biodiversity Initiative (AMMBI) Marine Microbes Project + Biomes of Australian DAR Soil Environments YON NSI NSI ROT PHB PHB KAI MAI MAI Evolution of the Marine Microbiome Initiative 2012 2014 2018 Australian Marine Microbe BPA Marine Microbes Project Biodiversity Initiative (AMMBI) DAR 2019 YON Marine Microbiome Initiative A new IMOS Facility! NSI NSI ROT • Sample processing & PHB PHB archiving KAI • DNA extractions MAI MAI Jodie van de Kamp Consortium of > 50 researchers from 10 universities and research institutes Contributed $910K DNA extraction: $90,000 (Marine Microbes Init. Facility) Bioinformatic position: $560,000 (Bioinformatics Sub-Facility) Coastal microbial observatory support: $260,000 Andrew Bissett Bioinformatics New IMOS Sub-Facility! • Genomics data processing Matt Smith • Workflows NSI YON The Australian DAR Microbiome dataset Dark Ocean PHB contains ~5,000
    [Show full text]
  • Phylogenetic Responses of Marine Free-Living Bacterial Community to Phaeocystis Globosa Bloom in Beibu Gulf, China
    fmicb-11-01624 July 14, 2020 Time: 17:42 # 1 ORIGINAL RESEARCH published: 16 July 2020 doi: 10.3389/fmicb.2020.01624 Phylogenetic Responses of Marine Free-Living Bacterial Community to Phaeocystis globosa Bloom in Beibu Gulf, China Nan Li1*, Huaxian Zhao1, Gonglingxia Jiang1, Qiangsheng Xu1, Jinli Tang1, Xiaoli Li1, Jiemei Wen1, Huimin Liu1, Chaowu Tang1, Ke Dong2 and Zhenjun Kang3* 1 Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China, 2 Department of Biological Sciences, Kyonggi University, Suwon-si, South Korea, 3 Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, China Phaeocystis globosa blooms are recognized as playing an essential role in shaping the structure of the marine community and its functions in marine ecosystems. In this study, we observed variation in the alpha diversity and composition of marine free-living bacteria during P. globosa blooms and identified key microbial community Edited by: assembly patterns during the blooms. The results showed that the Shannon index Olga Lage, was higher before the blooming of P. globosa in the subtropical bay. Marinobacterium University of Porto, Portugal (g-proteobacteria), Erythrobacter (a-proteobacteria), and Persicobacter (Cytophagales) Reviewed by: Xiaoqian Yu, were defined as the most important genera, and they were more correlated with University of Vienna, Austria environmental factors at the terminal stage of P. globosa blooms. Furthermore, different Catarina Magalhães, community assembly processes were observed. Both the mean nearest relatedness University of Porto, Portugal index (NRI) and nearest taxon index (NTI) revealed the dominance of deterministic *Correspondence: Nan Li factors in the non-blooming and blooming periods of P.
    [Show full text]
  • The Marine Microbiome an Untapped Source of Biodiversity and Biotechnological Potential
    springer.com Life Sciences : Microbiology Stal, Lucas J., Cretoiu, Mariana Silvia (Eds.) The Marine Microbiome An Untapped Source of Biodiversity and Biotechnological Potential and up-to-date review of marine microbial diversity and their habitats the role of marine microbial diversity in ecosystem function Presents novel products from marine microorganisms This book describes the state-of-the-art concerning the ‘marine microbiome’ and its uses in biotechnology. The first part discusses the diversity and ecology of marine microorganisms and viruses, including all three domains of life: Bacteria, Archaea, and Eukarya. It discusses whether marine microorganisms exist and, if so, why they might be unique. The second part presents selected marine habitats, their inhabitants and how they influence biogeochemical cycles, while the third discusses the utilization of marine microbial resources, including legal aspects, dissemination, and public awareness. The marine microbiome is the total of microorganisms and viruses in the ocean and seas and in any connected environment, including the seafloor Springer and marine animals and plants. The diversity of microbial life remains unquantified and largely 1st ed. 2016, XIV, 498 p. 43 unknown, and could represent a hidden treasure for human society. Accordingly, this book is 1st illus., 34 illus. in color. also intended to connect academics and industry, providing essential information for edition microbiologists from both fields. Order online at springer.com/booksellers Printed book Springer Nature Customer Service Center GmbH Hardcover Customer Service Tiergartenstrasse 15-17 Printed book 69121 Heidelberg Hardcover Germany ISBN 978-3-319-32998-7 T: +49 (0)6221 345-4301 £ 179,99 | CHF 236,00 | 199,99 € | [email protected] 219,99 € (A) | 213,99 € (D) Available Discount group Science (SC) Product category Contributed volume Other renditions Softcover ISBN 978-3-319-32999-4 Softcover ISBN 978-3-319-81418-6 Prices and other details are subject to change without notice.
    [Show full text]
  • Gene Exchange Networks Define Species-Like Units in Marine Prokaryotes
    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.10.291518; this version posted September 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Title: 2 Gene exchange networks define species-like units in marine prokaryotes 3 4 Authors: 5 R. Stepanauskas1*, J.M. Brown1, U. Mai2, O. Bezuidt1, M. Pachiadaki3, J. Brown1, S.J. Biller4, 6 P.M. Berube5, N.R. Record1, S. Mirarab6. 7 Affiliations: 8 1 Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, U.S.A. 9 2 Department of Computer Science and Engineering, University of California, San Diego, La 10 Jolla, California 92093, U.S.A. 11 3 Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, U.S.A. 12 4 Department of Biological Sciences, Wellesley College, Wellesley, Massachusetts 02481, 13 U.S.A. 14 5 Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Cambridge, Massachusetts 02142, U.S.A. 16 6 Department of Electrical and Computer Engineering, University of California, San Diego, La 17 Jolla, California 92093, U.S.A. 18 19 *Correspondence to: [email protected] 20 21 Page 1 of 26 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.10.291518; this version posted September 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • The Marine Microbiome Initiative
    The Marine Microbiome Initiative Justin Seymour, Martin Ostrowski, Mark Brown, Lev Bodrossy, Jodie van de Kamp, Andrew Bissett, Ana Lara-Lopez Consortium of > 50 researchers from 10 universities and research institutes Contributed $910K Bioinformatic position: $560,000 DNA extraction: $90,000 Coastal microbial observatory support: $260,000 Marine Microbes now an IMOS Facility! Seymour 2014 From Anthony Richardson’s talk on Wednesday: EOVs: Slides from Pier Buttigieg (via Ana Lara-Lopez) Emerging EOV: Microbial diversity and biomass Slides from Pier Buttigieg (via Ana Lara-Lopez) Evolution of the Marine Microbiome Initiative 2012 Australian Marine Microbe Biodiversity Initiative (AMMBI) NSI PHB MAI Evolution of the Marine Microbiome Initiative 2012 2014 Australian Marine Microbe BPA Marine Microbes Project Biodiversity Initiative (AMMBI) $1M DAR YON NSI NSI ROT PHB PHB KAI MAI MAI Evolution of the Marine Microbiome Initiative 2012 2014 2018 Australian Marine Microbe BPA Marine Microbes Project Biodiversity Initiative (AMMBI) DAR YON NSI NSI ROT PHB PHB KAI MAI MAI Evolution of the Marine Microbiome Initiative 2012 2014 2018 Australian Marine Microbe BPA Marine Microbes Project Biodiversity Initiative (AMMBI) Marine Microbes Project + Biomes of Australian DAR Soil Environments YON NSI NSI ROT PHB PHB KAI MAI MAI Evolution of the Marine Microbiome Initiative 2012 2014 2018 Australian Marine Microbe BPA Marine Microbes Project Biodiversity Initiative (AMMBI) DAR 2019 YON Marine Microbiome Facility NSI NSI ROT PHB PHB KAI MAI MAI Evolution
    [Show full text]
  • Charting the Complexity of the Marine Microbiome Through Single Cell Genomics
    Charting the Complexity of the Marine Microbiome through Single-Cell Genomics The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Pachiadaki, Maria G. et al. "Charting the Complexity of the Marine Microbiome through Single-Cell Genomics." Cell 179, 7 (December 2019): P1623-1635.e11 © 2019 Elsevier Inc As Published http://dx.doi.org/10.1016/j.cell.2019.11.017 Publisher Elsevier BV Version Author's final manuscript Citable link https://hdl.handle.net/1721.1/128866 Terms of Use Creative Commons Attribution-NonCommercial-NoDerivs License Detailed Terms http://creativecommons.org/licenses/by-nc-nd/4.0/ HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Cell. Author Manuscript Author manuscript; Manuscript Author available in PMC 2020 December 12. Published in final edited form as: Cell. 2019 December 12; 179(7): 1623–1635.e11. doi:10.1016/j.cell.2019.11.017. Charting the complexity of the marine microbiome through single cell genomics Maria G. Pachiadaki1,2, Julia M. Brown1, Joseph Brown1, Oliver Bezuidt1, Paul M. Berube3, Steven J. Biller3,6, Nicole J. Poulton1, Michael D. Burkart4, James J. La Clair4, Sallie W. Chisholm3,5, Ramunas Stepanauskas1,7,* 1Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, U.S.A. 2Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, U.S.A. 3Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, U.S.A. 4Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, U.S.A. 5Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, U.S.A.
    [Show full text]